Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 106, Issue 49, Pages 20746-20751Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0906500106
Keywords
cis-trans isomerization; left-handed helix; molecular dynamics; PPI; PPII
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Funding
- National Science Foundation Career [DMR-0348039, FRG-0804549]
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [804549] Funding Source: National Science Foundation
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The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle omega, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.
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